Online supplementary information

Advances in our structural understanding of orphan nuclear receptors

Nerea Gallastegui1, Jonathan A.G. Mackinnon1, Robert J. Fletterick2, and Eva Estébanez-Perpiñá1

1The Institute of Biomedicine of the University of Barcelona, Department of Biochemistry and Molecular

Biology, University of Barcelona, Baldiri Reixac 15-21, 08028 Barcelona, Spain

2The Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA,

USA

Corresponding author: Estébanez-Perpiñá, E. (E-mail: evaestebanez@ub.edu).

FIGURE S1

FIGURE S2

FIGURE S3

FIGURE S1: STRUCTURES OF ALL CLASSICAL AND ADOPTED NR-LBD IN THEIR STANDARD

ORIENTATION. . This figure shows the cartoon representation of the LBD structure of all classical and

adopted NR known to date. Additionally it accentuates the structural similarities observed in classical and

adopted NR in comparison with Figure 2 of the main text, where ONR show an array of structural differences

between themselves. Here we can observe the following structures in the different subfamilies: subfamily 1;

TRβ (PDB 1BSX) and RARα (PDB 3KMR), PPARδ (PDB 3GWX), LXRβ (PDB 1P8D), FXRβ (PDB 1OSH),

PXR (PDB 1NRL), CAR (PDB 1XV9), subfamily 2; RXRα (PDB 1FBY) and heterodimer structure of RXRα

with RARα (PDB 1DKF), subfamily 3; ERα (PDB 1ERE), GR (PDB 1P93) and AR (PDB 1T5Z) Amino acids

depicted in: dark blue are involved in the AF-2 groove, red presents the different areas of the NR which have

shown to be structurally different to the common canonical NR structure and in black are the different

peptides that have been co-crystallized with the NR. The ball and stick representation are those ligands that

have been seen in the structures.

FIGURE S2: COMPARISON OF ALL THE DOMAIN LENGTHS OF NR. Representation in scale of the

different domains of NR showing the difference of domain length of NRs, in white N-terminus domain, black

the DBD, dark grey the hinge and in light grey the LBD. Here, the domain sizes of ONR, which are shown in

bold and underlined, can be compared with those of the classical or adopted NR.

FIGURE S3: CARTOON REPRESENTATION OF THE THREE CRYSTAL STRUCTURES SOLVED TO

DATE OF FULL LENGTH MAMMALIAN NR, Cartoon representation of the full length crystal structure of a)

HNF4-α, (PDB 4IQR) b) PPARγ-RXRα, (PDB 3DZY) c) LXRβ-RXRα (PDB 4NQA). Up to date only three

mammalian NR full length structures have been elucidated, all in different conformations. Each individual

LBD is depicted in light and dark grey with the coactivator peptides shown in pink, the DBD are shown in

dark and light blue corresponding to each light and dark LBD. The DNA is found in cartoon representation in

cream color while the ligands are depicted in ball and stick format in yellow color for carbons and standard

coloring for other atoms.

Table S1: Structural data of ONR

NR PDB LBP (Å3)

Additional molecules-Binding site:no. res. (Å) H12 POS Surface LBP

ROR 1N831SOX

1.62.2

AGOAGO

720--

cholesterolcholesterol-3-O-sulfate

ROR1K4W1N4H1NQ7

1.92.11.5

AGOAGOAGO

760-820

SRC1-BOX2SRC1-BOX2SRC1-BOX3

stearic acidretinoic acidALRT 1550

ROR3L0L3KYT3L0J

1.72.42.4

AGOAGOAGO

1000SRC2-BOX2SRC2-BOX2SRC2-BOX2

25-hydroxycholesterole20-hydroxycholesterole22(R)-hydroxycholesterole

Rev-erb 3N00 2.6 REP <30NCOR1-BOX2

-

Rev-erb2V0V2V7C3CQV

2.42.41.9

NO H12NO H12NO H12

50-600---

--Protoporphyrin IX + Fe

HNF-4 1PZL1LV23FS14IQR

2.12.72.22.9

AGOAGOAGOAGO

440-680

SCR1-BOX2-PGC-1-BOX3TIF2-BOX2

myristic acidpalmitic acidmyristic acidmyristic acidFull length

HNF-4 1M7W 2.8AGO/ANTAGO

440 - Lauric acid

TR4 3P0U 3.0 REP 100 - -PNR 4LOG 2.7 REP 60 - -COUPTF-II 3CJW 1.5 REP 170 - -

ERR3D241XB72PJL

2.12.52.3

AGOAGOREP

40-630

PGC1 -BOX3PGC1 -BOX3-

--Indole compound1a

ERR

1S9P1S9Q1VJB2E2R2P7G2EWP2ZBS2GPU2P7Z2ZAS2P7A2ZKC1TFC1KV62GPO2GPP2GPV

2.12.23.21.62.12.31.81.72.52.02.31.72.42.72.02.62.9

ANTAGOANTAGONO H12AGOAGOREPAGOREPNo H12AGOAGOAGOAGOAGOAGOAGOANTAGO

200-1020

------------SRC-1-BOX2SRC-1-BOX2NRIP1-BOX5-SMRT-ID2

Diethylstibestrolcholic acid + 4hydroxytamoxifen4-hydroxytamoxifenBisphenol ABisphenol AGSK5182-4-hydroxytamoxifen4-hydroxytamoxifenCumylphenol4-chloro-3-methyl phenolBisphenol Z---GSK47164-hydroxytamoxifen

Nur77

3V3E3V3Q4JGV1YJE4KZI4KZJ4KZM

2.02.23.02.42.42.12.3

AGOAGOAGOAGOAGOAGOAGO

40-380

-TMYTHNP-DPDO--

-------

Nurr1 1OVL 2.2 AGO 30 - -

LRH-1 1PK51ZH73F5C1YUC1YOK3TX74DOR4DOS3PLZ

2.42.53.01.92.52.71.92.01.8

AGOAGOAGOAGOAGOAGOAGOAGOAGO

620-820

-SHP-BOX1DAX1 proteinSHP-BOX1TIF2-BOX3-CateninSHP-BOX1TIF2-BOX3

---phopholipidP6LP6LEPHPhosphatidylcholineGSK8470

TIF2-BOX3

SF-1

1YMT1YOW1YP01ZDT3F7D

1.23.01.52.12.2

AGOAGOAGOAGOAGO

220-1300

SHP-BOX1TIF2-BOX3SHP-BOX1TIF2-BOX3PGC1-

-PhosphatidylethanolPEFPEFPhospholipid (PC)

DAX1 3F5C 3.0 AGO 80LRH-1 protein

-

SHP 4NUF 2.8 REP 35EID-1 (91-105)

-

TABLE 1: LIST OF ALL THE ONR PDB FILES SOLVED SINCE 2003. Table contains the following

information i) Listing of all the latest ONR LDB-PDB files in the Protein Data Bank solved since 2003 ii)

structure data resolution, iii) visualized H12 poses: agonist (AGO), auto-repressed (REP), dislodged (DIS),

antagonist (ANTAGO), and devoid of a H12, iv) the LBP volume in Å3 v) the additional molecules binding to

either the AF-2 (peptides or proteins) binding site or the LBP.

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